Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4R1R

RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP AND EFFECTOR DTTP FROM ESCHERICHIA COLI

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005829	cellular_component	cytosol
A	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
A	0006457	biological_process	protein folding
A	0009185	biological_process	ribonucleoside diphosphate metabolic process
A	0009263	biological_process	deoxyribonucleotide biosynthetic process
A	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
A	0015949	biological_process	nucleobase-containing small molecule interconversion
A	0016491	molecular_function	oxidoreductase activity
A	0042802	molecular_function	identical protein binding
A	0044183	molecular_function	protein folding chaperone
B	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005829	cellular_component	cytosol
B	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
B	0006457	biological_process	protein folding
B	0009185	biological_process	ribonucleoside diphosphate metabolic process
B	0009263	biological_process	deoxyribonucleotide biosynthetic process
B	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
B	0015949	biological_process	nucleobase-containing small molecule interconversion
B	0016491	molecular_function	oxidoreductase activity
B	0042802	molecular_function	identical protein binding
B	0044183	molecular_function	protein folding chaperone
C	0004748	molecular_function	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0005971	cellular_component	ribonucleoside-diphosphate reductase complex
C	0006457	biological_process	protein folding
C	0009185	biological_process	ribonucleoside diphosphate metabolic process
C	0009263	biological_process	deoxyribonucleotide biosynthetic process
C	0009265	biological_process	2'-deoxyribonucleotide biosynthetic process
C	0015949	biological_process	nucleobase-containing small molecule interconversion
C	0016491	molecular_function	oxidoreductase activity
C	0042802	molecular_function	identical protein binding
C	0044183	molecular_function	protein folding chaperone

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE TTP A 762

Chain	Residue
A	ASP232
A	SER233
A	LEU234
A	ARG262
A	ILE268
A	ARG269
A	HIS275
A	THR276
B	SER249

site_id	AC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GDP A 763

Chain	Residue
A	THR209
A	SER224
A	CYS225
A	GLY253
A	ASN437
A	CYS439
A	GLU441
A	PRO621
A	SER622
A	GLU623
A	THR624
A	SER625

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE TTP B 762

Chain	Residue
A	SER249
B	ASP232
B	SER233
B	LEU234
B	ARG262
B	ILE268
B	ARG269
B	HIS275
B	THR276

site_id	AC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GDP B 763

Chain	Residue
B	THR209
B	SER224
B	CYS225
B	GLY253
B	ASN437
B	CYS439
B	GLU441
B	PRO621
B	SER622
B	GLU623
B	THR624
B	SER625

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE TTP C 762

Chain	Residue
C	ASP232
C	SER233
C	LEU234
C	SER249
C	ARG262
C	ILE268
C	ARG269
C	HIS275
C	THR276

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GDP C 763

Chain	Residue
C	THR209
C	SER224
C	CYS225
C	GLY253
C	ASN437
C	CYS439
C	GLU441
C	PRO621
C	SER622
C	GLU623
C	THR624
C	SER625

site_id	ACA
Number of Residues	6
Details	ACTIVE SITE, WITH SUBSTRATE GDP, THE REDOX CENTER, CYS A 225 AND CYS A 462, IN THE REDUCED FORM.

Chain	Residue
A	CYS225
A	CYS462
A	CYS439
A	ASN437
A	GLU441
A	GDP763

site_id	ACB
Number of Residues	6
Details	ACTIVE SITE, WITH SUBSTRATE GDP, THE REDOX CENTER, CYS B 225 AND CYS B 462, IN THE REDUCED FORM.

Chain	Residue
B	CYS439
B	ASN437
B	GLU441
C	GDP763
B	CYS225
B	CYS462

site_id	ACG
Number of Residues	6
Details	ACTIVE SITE, WITH SUBSTRATE GDP, THE REDOX CENTER, CYS C 225 AND CYS C 462, IN THE REDUCED FORM.

Chain	Residue
C	CYS225
C	CYS462
C	CYS439
C	ASN437
C	GLU441
B	GDP763

site_id	SEE
Number of Residues	1
Details	SPECIFICITY SITE WITH DTTP. OBSERVE THAT THE STRUCTURE IN PDB ENTRY 2R1R CONTAINS A MORE WELL-REFINED STRUCTURE WITH DTTP.

Chain	Residue
C	TTP762

site_id	SEI
Number of Residues	1
Details	SPECIFICITY SITE WITH DTTP. OBSERVE THAT THE STRUCTURE IN PDB ENTRY 2R1R CONTAINS A MORE WELL-REFINED STRUCTURE WITH DTTP.

Chain	Residue
B	TTP762

site_id	SES
Number of Residues	1
Details	SPECIFICITY SITE WITH DTTP. OBSERVE THAT THE STRUCTURE IN PDB ENTRY 2R1R CONTAINS A MORE WELL-REFINED STRUCTURE WITH DTTP.

Chain	Residue
A	TTP762

Functional Information from PROSITE/UniProt

site_id	PS00089
Number of Residues	23
Details	RIBORED_LARGE Ribonucleotide reductase large subunit signature. WeaLresikthGLRNstlSAlmP

Chain	Residue	Details
A	TRP599-PRO621

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Proton acceptor

Chain	Residue	Details
A	ASN437
A	GLU441
B	ASN437
B	GLU441
C	ASN437
C	GLU441

site_id	SWS_FT_FI2
Number of Residues	3
Details	ACT_SITE: Cysteine radical intermediate

Chain	Residue	Details
A	CYS439
B	CYS439
C	CYS439

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:9309223, ECO:0007744\|PDB:3R1R

Chain	Residue	Details
A	LYS9
C	GLU15
C	THR55
C	LYS91
A	GLU15
A	THR55
A	LYS91
B	LYS9
B	GLU15
B	THR55
B	LYS91
C	LYS9

site_id	SWS_FT_FI4
Number of Residues	21
Details	BINDING: BINDING => ECO:0000269\|PubMed:9309223, ECO:0007744\|PDB:4R1R

Chain	Residue	Details
A	THR209
B	ARG262
B	ARG269
B	ASN437
B	GLU441
B	GLU623
C	THR209
C	ASP232
C	ARG262
C	ARG269
C	ASN437
A	ASP232
C	GLU441
C	GLU623
A	ARG262
A	ARG269
A	ASN437
A	GLU441
A	GLU623
B	THR209
B	ASP232

site_id	SWS_FT_FI5
Number of Residues	6
Details	SITE: Important for hydrogen atom transfer

Chain	Residue	Details
A	CYS225
A	CYS462
B	CYS225
B	CYS462
C	CYS225
C	CYS462

site_id	SWS_FT_FI6
Number of Residues	6
Details	SITE: Important for electron transfer

Chain	Residue	Details
A	TYR730
A	TYR731
B	TYR730
B	TYR731
C	TYR730
C	TYR731

site_id	SWS_FT_FI7
Number of Residues	6
Details	SITE: Interacts with thioredoxin/glutaredoxin

Chain	Residue	Details
A	CYS754
A	CYS759
B	CYS754
B	CYS759
C	CYS754
C	CYS759

site_id	SWS_FT_FI8
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:18723842

Chain	Residue	Details
A	LYS283
B	LYS283
C	LYS283

Catalytic Information from CSA

site_id	CSA1
Number of Residues	5
Details	Annotated By Reference To The Literature 3r1r

Chain	Residue	Details
A	GLU441
A	CYS462
A	CYS439
A	CYS225
A	ASN437

site_id	CSA2
Number of Residues	5
Details	Annotated By Reference To The Literature 3r1r

Chain	Residue	Details
B	GLU441
B	CYS462
B	CYS439
B	CYS225
B	ASN437

site_id	CSA3
Number of Residues	5
Details	Annotated By Reference To The Literature 3r1r

Chain	Residue	Details
C	GLU441
C	CYS462
C	CYS439
C	CYS225
C	ASN437

site_id	MCSA1
Number of Residues
Details	M-CSA 918

Chain	Residue	Details
A	CYS225	proton donor
A	ASN437
A	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
A	GLU441	proton acceptor
A	CYS462
A	TYR730	pi-pi interaction, single electron relay
A	TYR731	pi-pi interaction, single electron relay

site_id	MCSA2
Number of Residues
Details	M-CSA 918

Chain	Residue	Details
B	CYS225	proton donor
B	ASN437
B	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
B	GLU441	proton acceptor
B	CYS462
B	TYR730	pi-pi interaction, single electron relay
B	TYR731	pi-pi interaction, single electron relay

site_id	MCSA3
Number of Residues
Details	M-CSA 918

Chain	Residue	Details
C	CYS225	proton donor
C	ASN437
C	CYS439	hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
C	GLU441	proton acceptor
C	CYS462
C	TYR730	pi-pi interaction, single electron relay
C	TYR731	pi-pi interaction, single electron relay

site_id	MCSA4
Number of Residues
Details	M-CSA 918

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)